According to the official TF2 blog
, Valve will be "removing all TF2 items that were earned using external idling applications", in a bid to stop players from cheating for the much sought after item drops and surprises.
The update goes on to say that it's only around 4.5% of the entire TF2 community who will be affected by this, and that anyone who was smart enough to take the "moral high road" will soon find a new hat in their inventory. As prior to this there was no precedent for third-party apps, Valve have decided to step it up with a zero tolerance stance.
This reminds me of when Blizzard finally took a similar stance to WoW third-party system cheaters...